diff --git a/skills/continuous-learning-v2/scripts/instinct-cli.py b/skills/continuous-learning-v2/scripts/instinct-cli.py
index 710f4c69..8d87513a 100755
--- a/skills/continuous-learning-v2/scripts/instinct-cli.py
+++ b/skills/continuous-learning-v2/scripts/instinct-cli.py
@@ -703,10 +703,47 @@ def cmd_status(args) -> int:
                 days_left = max(0, PENDING_TTL_DAYS - item["age_days"])
                 print(f"    - {item['name']} ({days_left}d remaining)")
 
+    # Legacy data warning
+    _warn_legacy_data()
+
     print(f"\n{'='*60}\n")
     return 0
 
 
+def _warn_legacy_data() -> None:
+    """Warn if legacy ~/.claude/homunculus/ contains data while the active
+    path has moved to the XDG directory."""
+    legacy_dir = Path.home() / ".claude" / "homunculus"
+    if legacy_dir == HOMUNCULUS_DIR:
+        return  # CLV2_HOMUNCULUS_DIR explicitly points at the legacy path
+    if not legacy_dir.is_dir():
+        return
+
+    # Count substantive files (skip empty dirs and the directory itself)
+    try:
+        legacy_files = [f for f in legacy_dir.rglob("*") if f.is_file()]
+    except (PermissionError, OSError):
+        print(f"\n  Note: legacy directory exists but cannot be read: {legacy_dir}", file=sys.stderr)
+        return
+    if not legacy_files:
+        return
+
+    migrate_script = Path(__file__).resolve().parent / "migrate-homunculus.sh"
+
+    print(f"\n{'!'*60}")
+    print("  LEGACY DATA DETECTED")
+    print(f"{'!'*60}")
+    print(f"  Found {len(legacy_files)} file(s) in legacy path:")
+    print(f"    {legacy_dir}")
+    print("  Active data directory:")
+    print(f"    {HOMUNCULUS_DIR}")
+    print()
+    print("  Run the migration script to move your data:")
+    print(f'    bash "{migrate_script}"')
+    print(f"  Or set CLV2_HOMUNCULUS_DIR={legacy_dir} to use the legacy path.")
+    print(f"{'!'*60}\n")
+
+
 def _print_instincts_by_domain(instincts: list[dict]) -> None:
     """Helper to print instincts grouped by domain."""
     by_domain = defaultdict(list)
diff --git a/tests/scripts/instinct-cli-projects.test.js b/tests/scripts/instinct-cli-projects.test.js
index 3ebd8651..d2d95161 100644
--- a/tests/scripts/instinct-cli-projects.test.js
+++ b/tests/scripts/instinct-cli-projects.test.js
@@ -219,6 +219,65 @@ test('projects merge deduplicates instincts, appends observations, and removes s
   }
 });
 
+test('status warns when legacy ~/.claude/homunculus contains files', () => {
+  const root = createTempDir();
+  try {
+    const legacyDir = path.join(root, 'home', '.claude', 'homunculus', 'instincts', 'personal');
+    fs.mkdirSync(legacyDir, { recursive: true });
+    fs.writeFileSync(path.join(legacyDir, 'old-instinct.yaml'), '---\nid: old\n---\nOld instinct.\n');
+
+    const result = runCli(root, ['status']);
+    assert.strictEqual(result.status, 0, result.stderr);
+    assert.match(result.stdout, /LEGACY DATA DETECTED/);
+    assert.match(result.stdout, /legacy path/i);
+    assert.match(result.stdout, /migration script/i);
+  } finally {
+    cleanupDir(root);
+  }
+});
+
+test('status does not warn when legacy dir is empty', () => {
+  const root = createTempDir();
+  try {
+    const legacyDir = path.join(root, 'home', '.claude', 'homunculus');
+    fs.mkdirSync(legacyDir, { recursive: true });
+
+    const result = runCli(root, ['status']);
+    assert.strictEqual(result.status, 0, result.stderr);
+    assert.doesNotMatch(result.stdout, /LEGACY DATA DETECTED/);
+  } finally {
+    cleanupDir(root);
+  }
+});
+
+test('status does not warn when no legacy dir exists', () => {
+  const root = createTempDir();
+  try {
+    const result = runCli(root, ['status']);
+    assert.strictEqual(result.status, 0, result.stderr);
+    assert.doesNotMatch(result.stdout, /LEGACY DATA DETECTED/);
+  } finally {
+    cleanupDir(root);
+  }
+});
+
+test('status does not warn when CLV2_HOMUNCULUS_DIR points at legacy path', () => {
+  const root = createTempDir();
+  try {
+    const legacyDir = path.join(root, 'home', '.claude', 'homunculus', 'instincts', 'personal');
+    fs.mkdirSync(legacyDir, { recursive: true });
+    fs.writeFileSync(path.join(legacyDir, 'active.yaml'), '---\nid: active\n---\nActive.\n');
+
+    const result = runCli(root, ['status'], {
+      env: { CLV2_HOMUNCULUS_DIR: path.join(root, 'home', '.claude', 'homunculus') },
+    });
+    assert.strictEqual(result.status, 0, result.stderr);
+    assert.doesNotMatch(result.stdout, /LEGACY DATA DETECTED/);
+  } finally {
+    cleanupDir(root);
+  }
+});
+
 test('status migrates legacy no-remote linked worktree project dirs to main worktree id', () => {
   const root = createTempDir();
   const repoParent = createTempDir();